Swirski FK, Berger CR, Figueiredo JL, Mempel TR, von Andrian UH, Pittet MJ, Weissleder R

A near-infrared cell tracker reagent for multiscopic in vivo imaging and quantification of leukocyte immune responses.
PLoS ONE. 2007;2(10):e1075 - PMID: 17957257 - PMCID: PMC2034600 - DOI: 10.1371/journal.pone.0001075

Gounaris E, Tung CH, Restaino C, Maehr R, Kohler R, Joyce JA, Plough HL, Barrett TA, Weissleder R, Khazaie K

Live imaging of cysteine-cathepsin activity reveals dynamics of focal inflammation, angiogenesis, and polyp growth.
PLoS ONE. 2008;3:e2916 - PMID: 18698347 - PMCID: PMC2488397 - DOI: 10.1371/journal.pone.0002916

Badr C, Hewett J, Breakefield X, Tannous B

A Highly Sensitive Assay for Monitoring the Secretory Pathway and ER Stress
PLoS ONE. 0;6:e571

Jeong JH, Wang Z, Guimaraes AS, Ouyang X, Figueiredo JL, Ding Z, Jiang S, Guney I, Kang GH, Shin E, Hahn WC, Loda MF, Abate-Shen C, Weissleder R, Chin L

BRAF activation initiates but does not maintain invasive prostate adenocarcinoma.
PLoS ONE. 2008;3(12):e3949 - PMID: 19079609 - PMCID: PMC2597248 - DOI: 10.1371/journal.pone.0003949

Vidarsson H, Westergren R, Heglind M, Blomqvist SR, Breton S, Enerback S

The forkhead transcription factor Foxi1 is a master regulator of vacuolar H-ATPase proton pump subunits in the inner ear, kidney and epididymis.
PLoS ONE. 2009;4(2):e4471 - PMID: 19214237 - PMCID: PMC2637605 - DOI: 10.1371/journal.pone.0004471

Wu Q, Sun CC, Lin HY, Babitt JL

Repulsive Guidance Molecule (RGM) Family Proteins Exhibit Differential Binding Kinetics for Bone Morphogenetic Proteins (BMPs).
PLoS ONE. 2012;7(9):e46307 - PMID: 23029472 - PMCID: PMC3459908 - DOI: 10.1371/journal.pone.0046307

Păunescu TG, Rodriguez S, Benz E, McKee M, Tyszkowski R, Albers MW, Brown D

Loss of the V-ATPase B1 Subunit Isoform Expressed in Non-Neuronal Cells of the Mouse Olfactory Epithelium Impairs Olfactory Function.
PLoS ONE. 2012;7(9):e45395 - PMID: 23028982 - PMCID: PMC3447883 - DOI: 10.1371/journal.pone.0045395

Wu X, Yung LM, Cheng WH, Yu PB, Babitt JL, Lin HY, Xia Y

Hepcidin Regulation by BMP Signaling in Macrophages Is Lipopolysaccharide Dependent.
PLoS ONE. 2012;7(9):e44622 - PMID: 23028567 - PMCID: PMC3441567 - DOI: 10.1371/journal.pone.0044622

Rice WL, Van Hoek AN, Păunescu TG, Huynh C, Goetze B, Singh B, Scipioni L, Stern LA, Brown D

High resolution helium ion scanning microscopy of the rat kidney.
PLoS ONE. 2013;8(3):e57051 - PMID: 23505418 - PMCID: PMC3591388 - DOI: 10.1371/journal.pone.0057051

Buys ES, Ko YC, Alt C, Hayton SR, Jones A, Tainsh LT, Ren R, Giani A, Clerté M, Abernathy E, Tainsh RE, Oh DJ, Malhotra R, Arora P, de Waard N, Yu B, Turcotte R, Nathan D, Scherrer-Crosbie M, Loomis SJ, Kang JH, Lin CP, Gong H, Rhee DJ, Brouckaert P, Wiggs JL, Gregory MS, Pasquale LR, Bloch KD, Ksander BR

Soluble Guanylate Cyclase α1-Deficient Mice: A Novel Murine Model for Primary Open Angle Glaucoma.
PLoS ONE. 2013;8(3):e60156 - PMID: 23527308 - PMCID: PMC3603933 - DOI: 10.1371/journal.pone.0060156

Giedt RJ, Koch PD, Weissleder R

Single Cell Analysis of Drug Distribution by Intravital Imaging.
PLoS ONE. 2013;8(4):e60988 - PMID: 23593370 - PMCID: PMC3622689 - DOI: 10.1371/journal.pone.0060988

Prabhakar S, Goto J, Zuang X, Sena-Esteves M, Bronson R, Brockmann J, Gianni D, Wojtkiewicz GR, Chen JW, Stemmer-Rachamimov A, Kwiatkowski DJ, Breakefield XO

Stochastic model of tsc1 lesions in mouse brain.
PLoS ONE. 2013;8(5):e64224 - PMID: 23696872 - PMCID: PMC3655945 - DOI: 10.1371/journal.pone.0064224

Feijó Delgado F, Cermak N, Hecht VC, Son S, Li Y, Knudsen SM, Olcum S, Higgins JM, Chen J, Grover WH, Manalis SR

Intracellular Water Exchange for Measuring the Dry Mass, Water Mass and Changes in Chemical Composition of Living Cells.
PLoS ONE. 2013;8(7):e67590 - PMID: 23844039 - PMCID: PMC3699654 - DOI: 10.1371/journal.pone.0067590

Pulli B, Ali M, Forghani R, Schob S, Hsieh KL, Wojtkiewicz G, Linnoila JJ, Chen JW

Measuring myeloperoxidase activity in biological samples.
PLoS ONE. 2013;8(7):e67976 - PMID: 23861842 - PMCID: PMC3702519 - DOI: 10.1371/journal.pone.0067976

Carlson AL, Fujisaki J, Wu J, Runnels JM, Turcotte R, Spencer JA, Celso CL, Scadden DT, Strom TB, Lin CP

Tracking single cells in live animals using a photoconvertible near-infrared cell membrane label.
PLoS ONE. 2013;8(8):e69257 - PMID: 23990881 - PMCID: PMC3753322 - DOI: 10.1371/journal.pone.0069257

Mortensen LJ, Levy O, Phillips JP, Stratton T, Triana B, Ruiz JP, Gu F, Karp JM, Lin CP

Quantification of Mesenchymal Stem Cell (MSC) Delivery to a Target Site Using In Vivo Confocal Microscopy.
PLoS ONE. 2013;8(10):e78145 - PMID: 24205131 - PMCID: PMC3812161 - DOI: 10.1371/journal.pone.0078145

Xia Z, Secor E, Chibnik LB, Bove RM, Cheng S, Chitnis T, Cagan A, Gainer VS, Chen PJ, Liao KP, Shaw SY, Ananthakrishnan AN, Szolovits P, Weiner HL, Karlson EW, Murphy SN, Savova GK, Cai T, Churchill SE, Plenge RM, Kohane IS, De Jager PL

Modeling disease severity in multiple sclerosis using electronic health records.
PLoS ONE. 2013;8(11):e78927 - PMID: 24244385 - PMCID: PMC3823928 - DOI: 10.1371/journal.pone.0078927

Kim E, Yang K, Weissleder R

Bioorthogonal Small Molecule Imaging Agents Allow Single-Cell Imaging of MET
PLoS ONE. 2013;8 (11):e81275 - PMID: 24265843 - PMCID: PMC3827223 - DOI: 10.1371/journal.pone.0081275

Meynard D, Sun CC, Wu Q, Chen W, Chen S, Nelson CN, Waters MJ, Babitt JL, Lin HY

Inflammation Regulates TMPRSS6 Expression via STAT5.
PLoS ONE. 2013;8(12):e82127 - PMID: 24376517 - PMCID: PMC3871639 - DOI: 10.1371/journal.pone.0082127

Elman JS, Murray RM, Wang F, Shen K, Gao S, Conway KE, Yarmush ML, Tannous BA, Weissleder R, Parekkadan B

Pharmacokinetics of natural and engineered secreted factors delivered by mesenchymal stromal cells.
PLoS ONE. 2014;9(2):e89882 - PMID: 24587097 - PMCID: PMC3931832 - DOI: 10.1371/journal.pone.0089882

Miranda KC, Bond DT, Levin JZ, Adiconis X, Sivachenko A, Russ C, Brown D, Nusbaum C, Russo LM

Massively parallel sequencing of human urinary exosome/microvesicle RNA reveals a predominance of non-coding RNA.
PLoS ONE. 2014;9(5):e96094 - PMID: 24816817 - PMCID: PMC4015934 - DOI: 10.1371/journal.pone.0096094

Mehan WA, González RG, Buchbinder BR, Chen JW, Copen WA, Gupta R, Hirsch JA, Hunter GJ, Hunter S, Johnson JM, Kelly HR, Larvie M, Lev MH, Pomerantz SR, Rapalino O, Rincon S, Romero JM, Schaefer PW, Shah V

Optimal Brain MRI Protocol for New Neurological Complaint.
PLoS ONE. 2014;9(10):e110803 - PMID: 25343371 - PMCID: PMC4208779 - DOI: 10.1371/journal.pone.0110803

Hsieh LC, Chen JW, Wang LY, Tsang YM, Shueng PW, Liao LJ, Lo WC, Lin YC, Tseng CF, Kuo YS, Jhuang JY, Tien HJ, Juan HF, Hsieh CH

Predicting the severity and prognosis of trismus after intensity-modulated radiation therapy for oral cancer patients by magnetic resonance imaging.
PLoS ONE. 2014;9(3):e92561 - PMID: 24658376 - PMCID: PMC3962418 - DOI: 10.1371/journal.pone.0092561

Kessinger CW, Kim JW, Henke PK, Thompson B, McCarthy JR, Hara T, Sillesen M, Margey RJ, Libby P, Weissleder R, Lin CP, Jaffer FA

Statins Improve the Resolution of Established Murine Venous Thrombosis: Reductions in Thrombus Burden and Vein Wall Scarring.
PLoS ONE. 2015;10(2):e0116621 - PMID: 25680183 - PMCID: PMC4334538 - DOI: 10.1371/journal.pone.0116621

Azroyan A, Cortez-Retamozo V, Bouley R, Liberman R, Ruan YC, Kiselev E, Jacobson KA, Pittet MJ, Brown D, Breton S

Renal Intercalated Cells Sense and Mediate Inflammation via the P2Y14 Receptor.
PLoS ONE. 2015;10(3):e0121419 - PMID: 25799465 - PMCID: PMC4370445 - DOI: 10.1371/journal.pone.0121419

Rotem A, Ram O, Shoresh N, Sperling RA, Schnall-Levin M, Zhang H, Basu A, Bernstein BE, Weitz DA

High-Throughput Single-Cell Labeling (Hi-SCL) for RNA-Seq Using Drop-Based Microfluidics.
PLoS ONE. 2015;10(5):e0116328 - PMID: 26000628 - PMCID: PMC4441486 - DOI: 10.1371/journal.pone.0116328

Abazari A, Meimetis LG, Budin G, Bale SS, Weissleder R, Toner M

Engineered Trehalose Permeable to Mammalian Cells.
PLoS ONE. 2015;10(6):e0130323 - PMID: 26115179 - PMCID: PMC4482662 - DOI: 10.1371/journal.pone.0130323

Chung HJ, Pellegrini KL, Chung J, Wanigasuriya K, Jayawardene I, Lee K, Lee H, Vaidya VS, Weissleder R

Nanoparticle Detection of Urinary Markers for Point-of-Care Diagnosis of Kidney Injury.
PLoS ONE. 2015;10(7):e0133417 - PMID: 26186708 - PMCID: PMC4506142 - DOI: 10.1371/journal.pone.0133417

Liao KP, Ananthakrishnan AN, Kumar V, Xia Z, Cagan A, Gainer VS, Goryachev S, Chen P, Savova GK, Agniel D, Churchill S, Lee J, Murphy SN, Plenge RM, Szolovits P, Kohane I, Shaw SY, Karlson EW, Cai T

Methods to Develop an Electronic Medical Record Phenotype Algorithm to Compare the Risk of Coronary Artery Disease across 3 Chronic Disease Cohorts.
PLoS ONE. 2015;10(8):e0136651 - PMID: 26301417 - PMCID: PMC4547801 - DOI: 10.1371/journal.pone.0136651

Rice WL, Li W, Mamuya F, McKee M, Păunescu TG, Lu HA

Polarized Trafficking of AQP2 Revealed in Three Dimensional Epithelial Culture.
PLoS ONE. 2015;10(7):e0131719 - PMID: 26147297 - PMCID: PMC4493001 - DOI: 10.1371/journal.pone.0131719

Sosulski A, Horn H, Zhang L, Coletti C, Vathipadiekal V, Castro CM, Birrer MJ, Nagano O, Saya H, Lage K, Donahoe PK, Pépin D

CD44 Splice Variant v8-10 as a Marker of Serous Ovarian Cancer Prognosis.
PLoS ONE. 2016;11(6):e0156595 - PMID: 27253518 - PMCID: PMC4890777 - DOI: 10.1371/journal.pone.0156595

Vafai SB, Mevers E, Higgins KW, Fomina Y, Zhang J, Mandinova A, Newman D, Shaw SY, Clardy J, Mootha VK

Natural Product Screening Reveals Naphthoquinone Complex I Bypass Factors.
PLoS ONE. 2016;11(9):e0162686 - PMID: 27622560 - PMCID: PMC5021346 - DOI: 10.1371/journal.pone.0162686

Miller MA, Feng XJ, Li G, Rabitz HA

Identifying biological network structure, predicting network behavior, and classifying network state with High Dimensional Model Representation (HDMR).
PLoS ONE. 2012;7(6):e37664 - PMID: 22723838 - PMCID: PMC3377689 - DOI: 10.1371/journal.pone.0037664

Leming M, Das S, Im H

Adversarial confound regression and uncertainty measurements to classify heterogeneous clinical MRI in Mass General Brigham.
PLoS ONE. 2023;18(3):e0277572 - PMID: 36862751 - PMCID: PMC9980829 - DOI: 10.1371/journal.pone.0277572

Yoon BC, Pomerantz SR, Mercaldo ND, Goyal S, L'Italien EM, Lev MH, Buch KA, Buchbinder BR, Chen JW, Conklin J, Gupta R, Hunter GJ, Kamalian SC, Kelly HR, Rapalino O, Rincon SP, Romero JM, He J, Schaefer PW, Do S, González RG

Incorporating algorithmic uncertainty into a clinical machine deep learning algorithm for urgent head CTs.
PLoS ONE. 2023;18(3):e0281900 - PMID: 36913348 - PMCID: PMC10010506 - DOI: 10.1371/journal.pone.0281900

Tokarz D, Cisek R, Wein MN, Turcotte R, Haase C, Yeh SA, Bharadwaj S, Raphael AP, Paudel H, Alt C, Liu TM, Kronenberg HM, Lin CP

Intravital imaging of osteocytes in mouse calvaria using third harmonic generation microscopy.
PLoS ONE. 2017;12(10):e0186846 - PMID: 29065178 - PMCID: PMC5655444 - DOI: 10.1371/journal.pone.0186846

Arystarkhova E, Bouley R, Liu YB, Sweadner KJ

Impaired AQP2 trafficking in Fxyd1 knockout mice: A role for FXYD1 in regulated vesicular transport.
PLoS ONE. 2017;12(11):e0188006 - PMID: 29155857 - PMCID: PMC5695786 - DOI: 10.1371/journal.pone.0188006

Sahin A, Sanchez C, Bullain S, Waterman P, Weissleder R, Carter BS

Development of third generation anti-EGFRvIII chimeric T cells and EGFRvIII-expressing artificial antigen presenting cells for adoptive cell therapy for glioma.
PLoS ONE. 2018;13(7):e0199414 - PMID: 29975720 - PMCID: PMC6033533 - DOI: 10.1371/journal.pone.0199414

Nair AV, Yanhong W, Paunescu TG, Bouley R, Brown D

Sex-dependent differences in water homeostasis in wild-type and V-ATPase B1-subunit deficient mice.
PLoS ONE. 2019;14(8):e0219940 - PMID: 31386675 - PMCID: PMC6684071 - DOI: 10.1371/journal.pone.0219940

Chin LY, Carroll C, Raigani S, Detelich DM, Tessier SN, Wojtkiewicz GR, Schmidt SP, Weissleder R, Yeh H, Uygun K, Parekkadan B

Ex vivo perfusion-based engraftment of genetically engineered cell sensors into transplantable organs.
PLoS ONE. 2019;14(12):e0225222 - PMID: 31790444 - PMCID: PMC6886851 - DOI: 10.1371/journal.pone.0225222

Peng S, Wang JW, Karanam B, Wang C, Huh WK, Alvarez RD, Pai SI, Hung CF, Wu TC, Roden RB

Sequential cisplatin therapy and vaccination with HPV16 E6E7L2 fusion protein in saponin adjuvant GPI-0100 for the treatment of a model HPV16+ cancer.
PLoS ONE. 2015;10(1):e116389 - PMID: 25560237 - PMCID: PMC4283968 - DOI: 10.1371/journal.pone.0116389

Wu JW, Jung Y, Yeh SA, Seo Y, Runnels JM, Burns CS, Mizoguchi T, Ito K, Spencer JA, Lin CP

Intravital fluorescence microscopy with negative contrast.
PLoS ONE. 2021;16(8):e0255204 - PMID: 34351959 - PMCID: PMC8341626 - DOI: 10.1371/journal.pone.0255204

Wildgruber M, Lee H, Chudnovskiy A, Yoon T, Etzrodt M, Pittet M, Nahrendorf M, Croce K, Libby P, Weissleder R, Swirski F

Monocyte subset dynamics in human atherosclerosis can be profiled with magnetic nano-sensors.
PLoS ONE. 2009;4(5):e5663 - PMID: 19461894 - PMCID: PMC2680949 - DOI: 10.1371/journal.pone.0005663

Wadlow RC, Wittner BS, Finley SA, Bergquist H, Upadhyay R, Finn S, Loda M, Mahmood U, Ramaswamy S

Systems-level modeling of cancer-fibroblast interaction.
PLoS ONE. 2009;4(9):e6888 - PMID: 19727395 - PMCID: PMC2731225 - DOI: 10.1371/journal.pone.0006888

Thurber GM, Figueiredo JL, Weissleder R

Multicolor Fluorescent Intravital Live Microscopy (FILM) for Surgical Tumor Resection in a Mouse Xenograft Model.
PLoS ONE. 2009;4(11):e8053 - PMID: 19956597 - PMCID: PMC2779447 - DOI: 10.1371/journal.pone.0008053

Miranda KC, Karet FE, Brown D

An Extended Nomenclature for Mammalian V-ATPase Subunit Genes and Splice Variants.
PLoS ONE. 2010;5(3):e9531 - PMID: 20224822 - PMCID: PMC2835735 - DOI: 10.1371/journal.pone.0009531

Bratlie KM, Dang TT, Lyle S, Nahrendorf M, Weissleder R, Langer R, Anderson DG

Rapid biocompatibility analysis of materials via in vivo fluorescence imaging of mouse models.
PLoS ONE. 2010;5(4):e10032 - PMID: 20386609 - PMCID: PMC2850367 - DOI: 10.1371/journal.pone.0010032

Berny MA, Munnix IC, Auger JM, Schols SE, Cosemans JM, Panizzi P, Bock PE, Watson SP, McCarty OJ, Heemskerk JW

Spatial distribution of factor Xa, thrombin, and fibrin(ogen) on thrombi at venous shear.
PLoS ONE. 2010;5(4):e10415 - PMID: 20454680 - PMCID: PMC2861630 - DOI: 10.1371/journal.pone.0010415

Gibert Y, Lattanzi VJ, Zhen AW, Vedder L, Brunet F, Faasse SA, Babitt JL, Lin HY, Hammerschmidt M, Fraenkel PG

BMP Signaling Modulates Hepcidin Expression in Zebrafish Embryos Independent of Hemojuvelin.
PLoS ONE. 2011;6(1):e14553 - PMID: 21283739 - PMCID: PMC3024971 - DOI: 10.1371/journal.pone.0014553

Thurber GM, Weissleder R

A Systems Approach for Tumor Pharmacokinetics
PLoS ONE. 2011;6(9):e24696 - PMID: 21935441 - PMCID: PMC3173470 - DOI: 10.1371/journal.pone.0024696
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